I've seen over 30 unique magical girl works and in all of them I can't recall a single one where the internet has played any kind of important role. I'm probably missing something like Corrector Yui, but I've noticed that the internet almost never has a role in even a single episode of a show like Precure.

There's so much potential for the villains to exploit this to target lazy kids who spend all day browsing the internet (or if it's an adult-targeted show, a jab at Otaku)

Those viruses that send fake IM messages to people in your contact list could be the work of a monster of the week, and upon clicking the link a swirling hypno-symbol appears on the screen.

The villains and their monsters could use the internet to travel the world (also known as Japan) to cause trouble in different places, popping in and out of monitors as they please.

I can see why shows like Precure might not do this sort of thing. They probably don't want kids being encouraged to spend long periods of time on the internet. : P

There's Nurse Witch Komugi who takes a few episodes to do some otaku/internet meme jokes (alot of their more humorous jokes come from taking jabs at otaku culture tbh.)

There's also an internet/computer focused episode of the Magical Girl Pretty Sammy OVA, complete with an evil anime Bill Gates

The manga Cyber Idol Mink is a cute little story about a girl who uses a computer program from the future to transform into an idol

Also, Shoujo Kesshou KokoLogical, is a manga that just recently ended in Nakayoshi. It features a girl who starts visiting the cyber world known as BOX and has to try and save it for some reason (I've only read it RAW) and can transform into various dance-themed costumes. I think it has alot of potential for a cute new franchise, but it ended kind of abruptly (which leads me to believe it wasn't popular with readers, so they had the manga-ka rush a finale) so it probably wont happen